OverCOVID: an integrative web portal for SARS-CoV-2 bioinformatics resources

Abstract

Outbreaks of COVID-19 caused by the novel coronavirus SARS-CoV-2 is still a threat to global human health. In order to understand the biology of SARS-CoV-2 and developing drug against COVID-19, a vast amount of genomic, proteomic, interatomic, and clinical data is being generated, and the bioinformatics researchers produced databases, webservers and tools to gather those publicly available data and provide an opportunity of analyzing such data. However, these bioinformatics resources are scattered and researchers need to find them from different resources discretely. To facilitate researchers in finding the resources in one frame, we have developed an integrated web portal called OverCOVID (http://bis.zju.edu.cn/overcovid/). The publicly available webservers, databases and tools associated with SARS-CoV-2 have been incorporated in the resource page. In addition, a network view of the resources is provided to display the scope of the research. Other information like SARS-CoV-2 strains is visualized and various layers of interaction resources is listed in distinct pages of the web portal. As an integrative web portal, the OverCOVID will help the scientist to search the resources and accelerate the clinical research of SARS-CoV-2.

Keywords: COVID-19; SARS-CoV-2; bioinformatics resources; coronavirus.

Figure 1:

Timeline and basic properties of seven human coronaviruses. Two blue panels list alpha-coronavirus and the five pink panels list beta-coronavirus. All the boxes summarize the year of identification, location of first reported case, origin or natural host of the virus, genome length of virus, receptor, cleavage of the receptor, and major proteins of the respective human coronavirus. The left parts of the boxes present the main hosts for the corresponding coronaviruses. Two beta-coronaviruses, HCoV-OC43 and HCoV-HKU1 originate in mice and belong to hemagglutinin-esterase (HE) structural protein along with S, E, M and N. Other five viruses originated in bats and have only four major proteins S, E, M and N.

Figure 2:

Overview of the OverCOVID web portal. (A) Resources page contains SARS-CoV-2 related online resources with resource name, resource type, features of the resources, brief description, URL of the resources and publication link. It facilitates users to search the desire resources by typing the resource name or the keywords in the search box. (B) SARS-CoV-2 phylogeny. It uses the sequence data from GISAID and shows the development of each strain of the virus since the beginning of the spread of the virus. It also provides a comparison of different nomenclature systems, including the marker gene variants representing for each virus strain. (C) Network view of various resources from different aspects to accelerate research of SARS-CoV-2. An additional network view of the resources is provided to visually indicate the scope of research for each database/tool and to intuitively present extra information. (D) Resources of various layers of interactions among the viruses and human hosts. The interaction resources page provides information on the resources for each type of molecular interaction as well as the corresponding link of the source site.

Figure 3:

Bioinformatics resources and information on SARS-CoV-2 in the OverCOVID web portal.